October 09, 2010

ADMIXTURE in the New World

Here is the result of running ADMIXTURE on ~450K markers on six HapMap-3 populations; left-to-right: African Americans from the Southwest (ASW), Utah Whites (CEU), Beijing Chinese (CHB), Mexicans from Los Angeles (MEX),Toscans (TSI), and Yoruban from Nigeria (YRI).

Here are the admixture proportions (in %):

It is obvious, however, from the ADMIXTURE plot above, and the triangle plots below (for ASW and MEX), that the admixture is not uniformly distributed.

Notice the two African American individuals with substantial Amerindian admixture (14 and 29%), while the rest are a simple 2-way mix of Europeans and Sub-Saharans with minor Amerindian admixture in some of them. The standard deviation of European admixture is 8.3%, lower than in Mexicans.

Mexicans are variable in terms of their European-Amerindian mix, but with less variable tiny Sub-Saharan component (0.6% with a standard deviation of 1.2%). This is probably due to the fact that blacks were absorbed earlier in Mexico, while European-Amerindian social stratification and continued European immigration has fueled the retention of considerable variation. European admixture in Mexicans is 27.7% on average, but with a standard deviation of 24.0% and minimum/maximum value of 0.0 to 90.5% in the sample I am considering.

Eva Longoria, for example, who recently learned that she is 70% European in "Faces of America" belongs to the top-5% of Mexican American "European-ness", although there is probably considerable variation of Mexican Americans within the country.

Very nice. Your previous posts about using ADMIXTURE on the HGDP samples left me wondering, because Rosenberg had already done just that and well, your results seemed to just confirm those from his study. But these new ADMIXTURE results you're posting on the HapMap3 samples are something novel, and the results are very interesting.

How was the American Indian genetic cluster determined? On the basis of the Mexican samples? The results are based only on these 6 populations, right? The HGDP samples weren't used in any way to generate these results?

The results show Mexicans in Los Angeles, whom I think tend to be more from central Mexico (not too exaggerated, either), and they're broadly ok, but the European ancestry seems rather low at just 28%, I would've expected more like 35% judging from their sex chromosomes, and their black ancestry also seems low at 0,6%, I would've expected 2% to 3% because of same. A previous autosomal study found them to have 40% European ancestry, I think it was done on people from Mexico City. I wonder if this possible slight inaccuracy in the results, in contrast with the highly precise East Asian results, might be due to the ADMIXTURE program having to figure out the American Indian genetic cluster from mixed up samples (Mexicans), while it had perfect 100% East Asian samples to decypher that genetic cluster.

Another accuracy of this plot is that also Yorubas show up racially completely pure this time (in the previous plot they misleadingly showed very small "Caucasoid admixture" probably due to being tested together with Negroids from East Africa, who may really be Caucasoid-admixed).

As to Argiedude's question, if a completely or almost pure Amerindian population had been used as a proxy for Amerindianness and Mexicans had been compared to them in addition to the extant tested populations, a more accurate result might have shown up for Mexicans, then maybe the tested Caucasoid populations would have shown up racially completely pure.

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